SMED30025141

Overview
NameSMED30025141
Smed IDSMED30025141
Length (bp)1893
Neoblast Clusters

Zeng et. al., 2018



▻ Overview

▻ Neoblast Population

▻ Sub-lethal Irradiated Surviving X1 and X2 Cell Population

 

 

Overview

 

Single cell RNA-seq of pluripotent neoblasts and its early progenies


We isolated X1 neoblasts cells enriched in high piwi-1 expression (Neoblast Population), and profiled ∼7,614 individual cells via scRNA-seq. Unsupervised analyses uncovered 12 distinct classes from 7,088 high-quality cells. We designated these classes Nb1 to Nb12 and ordered them based on high (Nb1) to low (Nb12) piwi-1 expression levels. We further defined groups of genes that best classified the cells parsed into 12 distinct cell clusters to generate a scaled expression heat map of discriminative gene sets for each cluster. Expression of each cluster’s gene signatures was validated using multiplex fluorescence in situ hybridization (FISH) co-stained with piwi-1 and largely confirmed the cell clusters revealed by scRNA-seq.

We also tested sub-lethal irradiation exposure. To profile rare pluripotent stem cells (PSCs) and avoid interference from immediate progenitor cells, we determined a time point after sub-lethal irradiation (7 DPI) with minimal piwi-1+ cells, followed by isolation and single-cell RNA-seq of 1,200 individual cells derived from X1 (Piwi-1 high) and X2 (Piwi-1 low) cell populations (Sub-lethal Irradiated Surviving X1 and X2 Cell Population)



Explore this single cell expression dataset with our NB Cluster Shiny App



 

Neoblast Population

 

t-SNE plot shows two-dimensional representation of global gene expression relationships among all neoblasts (n = 7,088 after filter). Cluster identity was assigned based on the top 10 marker genes of each cluster (Table S2), followed by inspection of RNA in situ hybridization patterns. Neoblast groups, Nb.


Expression of SMED30025141 (SMED30025141) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30025141 (SMED30025141) in cells (dots) of each of the 12 neoblast clusters.

 

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Sub-lethal Irradiated Surviving X1 and X2 Cell Population

 

t-SNE plot of surviving X1 and X2 cells (n = 1,039 after QC filter) after sub-lethal irradiation. Colors indicate unbiased cell classification via graph-based clustering. SL, sub-lethal irradiated cell groups.

Expression of SMED30025141 (SMED30025141) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30025141 (SMED30025141) in cells (dots) of each of the 10 clusters of sub-leathally irradiated X1 and X2 cells.

 

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Embryonic Expression

Davies et. al., 2017

Hover the mouse over a column in the graph to view average RPKM values per sample.
Sort Descending | Sort Ascending | Only Non-Zero Values | Tile/Chart | Reset

Embryonic Stages: Y: yolk. S2-S8: Stages 2-8. C4: asexual adult. SX: virgin, sexually mature adult.
For further information about sample preparation and analysis for the single animal RNA-Seq experiment, please refer to the Materials and Methods

 

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Anatomical Expression

PAGE et. al., 2020



SMED30025141

has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGE



PAGE Curations: 12

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
X1 cellSMED30025141SMESG000076211.1 SMESG000047610.1 SmedASXL_008453SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
X2 cellSMED30025141SMESG000076211.1 SMESG000047610.1 SmedASXL_008453SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
pharynxSMED30025141SMESG000076211.1 SMESG000047610.1 dd_Smed_v4_2124_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30025141SMESG000076211.1 SMESG000047610.1 dd_Smed_v4_2124_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
gutSMED30025141SMESG000076211.1 SMESG000047610.1 dd_Smed_v4_2124_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30025141SMESG000076211.1 SMESG000047610.1 dd_Smed_v4_2124_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30025141SMESG000076211.1 SMESG000047610.1 dd_Smed_v4_2124_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30025141SMESG000076211.1 SMESG000047610.1 dd_Smed_v4_2124_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30025141SMESG000076211.1 SMESG000047610.1 dd_Smed_v4_2124_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
muscle cellSMED30025141SMESG000076211.1 SMESG000047610.1 dd_Smed_v4_2124_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30025141SMESG000076211.1 SMESG000047610.1 Contig37074newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30025141SMESG000076211.1 SMESG000047610.1 Contig37074uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30025141 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.004254:41764..43856 -9360
Homology
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BLAST of SMED30025141 vs. Planmine SMEST
Match: SMESG000076211.1 (SMESG000076211.1)

HSP 1 Score: 376.326 bits (965), Expect = 1.845e-126
Identity = 295/295 (100.00%), Postives = 295/295 (100.00%), Query Frame = 3 
Query:  129 PFNKFEDRSPKEDFPERGFRVSRRPIGNFSKNXXXXXXXXXXXXXXXXXXXXFXXXXXXXXXXXXXXXXXXXFGSMRRSPVDYRKDISRSRAISPPRKEYVMRDISPRNRDISPRMRDIEXXXXXXXXXXXXXXXXXXXXXXXSRNFESRNRDGRRDYSPNARDRHFSPVRYQHDRYEYSPPRSRNYERESFPDRRRNDVXXXXXXXXXXXXXXXXXXFRPRGGRFNSQRGNTRGRDNLNRFDSNQRNNFNRARDESSMRRGHNNDNPKRKVEQVPNSGIPPQKKSRDSSFDTSP 1013
            PFNKFEDRSPKEDFPERGFRVSRRPIGNFSKNYSRDEYRQRDERRDSYERDSFRQRESRRDPRERLRGRDREFGSMRRSPVDYRKDISRSRAISPPRKEYVMRDISPRNRDISPRMRDIEPRIRDMEPRMRDMDPRFRDYPPRSRNFESRNRDGRRDYSPNARDRHFSPVRYQHDRYEYSPPRSRNYERESFPDRRRNDVRSFNSRENREYRSRSPNNFRPRGGRFNSQRGNTRGRDNLNRFDSNQRNNFNRARDESSMRRGHNNDNPKRKVEQVPNSGIPPQKKSRDSSFDTSP
Sbjct:   25 PFNKFEDRSPKEDFPERGFRVSRRPIGNFSKNYSRDEYRQRDERRDSYERDSFRQRESRRDPRERLRGRDREFGSMRRSPVDYRKDISRSRAISPPRKEYVMRDISPRNRDISPRMRDIEPRIRDMEPRMRDMDPRFRDYPPRSRNFESRNRDGRRDYSPNARDRHFSPVRYQHDRYEYSPPRSRNYERESFPDRRRNDVRSFNSRENREYRSRSPNNFRPRGGRFNSQRGNTRGRDNLNRFDSNQRNNFNRARDESSMRRGHNNDNPKRKVEQVPNSGIPPQKKSRDSSFDTSP 319
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BLAST of SMED30025141 vs. Planmine SMEST
Match: SMESG000076211.1 (SMESG000076211.1)

HSP 1 Score: 283.493 bits (724), Expect = 4.273e-91
Identity = 246/246 (100.00%), Postives = 246/246 (100.00%), Query Frame = 3 
Query:  129 PFNKFEDRSPKEDFPERGFRVSRRPIGNFSKNXXXXXXXXXXXXXXXXXXXXFXXXXXXXXXXXXXXXXXXXFGSMRRSPVDYRKDISRSRAISPPRKEYVMRDISPRNRDISPRMRDIEXXXXXXXXXXXXXXXXXXXXXXXSRNFESRNRDGRRDYSPNARDRHFSPVRYQHDRYEYSPPRSRNYERESFPDRRRNDVXXXXXXXXXXXXXXXXXXFRPRGGRFNSQRGNTRGRDNLNRFDSNQ 866
            PFNKFEDRSPKEDFPERGFRVSRRPIGNFSKNYSRDEYRQRDERRDSYERDSFRQRESRRDPRERLRGRDREFGSMRRSPVDYRKDISRSRAISPPRKEYVMRDISPRNRDISPRMRDIEPRIRDMEPRMRDMDPRFRDYPPRSRNFESRNRDGRRDYSPNARDRHFSPVRYQHDRYEYSPPRSRNYERESFPDRRRNDVRSFNSRENREYRSRSPNNFRPRGGRFNSQRGNTRGRDNLNRFDSNQ
Sbjct:   25 PFNKFEDRSPKEDFPERGFRVSRRPIGNFSKNYSRDEYRQRDERRDSYERDSFRQRESRRDPRERLRGRDREFGSMRRSPVDYRKDISRSRAISPPRKEYVMRDISPRNRDISPRMRDIEPRIRDMEPRMRDMDPRFRDYPPRSRNFESRNRDGRRDYSPNARDRHFSPVRYQHDRYEYSPPRSRNYERESFPDRRRNDVRSFNSRENREYRSRSPNNFRPRGGRFNSQRGNTRGRDNLNRFDSNQ 270
[Close]
BLAST of SMED30025141 vs. Planmine SMEST
Match: SMESG000047610.1 (SMESG000047610.1)

HSP 1 Score: 236.884 bits (603), Expect = 2.087e-73
Identity = 200/200 (100.00%), Postives = 200/200 (100.00%), Query Frame = 3 
Query:  129 PFNKFEDRSPKEDFPERGFRVSRRPIGNFSKNXXXXXXXXXXXXXXXXXXXXFXXXXXXXXXXXXXXXXXXXFGSMRRSPVDYRKDISRSRAISPPRKEYVMRDISPRNRDISPRMRDIEXXXXXXXXXXXXXXXXXXXXXXXSRNFESRNRDGRRDYSPNARDRHFSPVRYQHDRYEYSPPRSRNYERESFPDRRRNDV 728
            PFNKFEDRSPKEDFPERGFRVSRRPIGNFSKNYSRDEYRQRDERRDSYERDSFRQRESRRDPRERLRGRDREFGSMRRSPVDYRKDISRSRAISPPRKEYVMRDISPRNRDISPRMRDIEPRIRDMEPRMRDMDPRFRDYPPRSRNFESRNRDGRRDYSPNARDRHFSPVRYQHDRYEYSPPRSRNYERESFPDRRRNDV
Sbjct:   25 PFNKFEDRSPKEDFPERGFRVSRRPIGNFSKNYSRDEYRQRDERRDSYERDSFRQRESRRDPRERLRGRDREFGSMRRSPVDYRKDISRSRAISPPRKEYVMRDISPRNRDISPRMRDIEPRIRDMEPRMRDMDPRFRDYPPRSRNFESRNRDGRRDYSPNARDRHFSPVRYQHDRYEYSPPRSRNYERESFPDRRRNDV 224
[Close]
BLAST of SMED30025141 vs. Planmine SMEST
Match: SMESG000047610.1 (SMESG000047610.1)

HSP 1 Score: 166.392 bits (420), Expect = 8.231e-48
Identity = 163/163 (100.00%), Postives = 163/163 (100.00%), Query Frame = 3 
Query:  129 PFNKFEDRSPKEDFPERGFRVSRRPIGNFSKNXXXXXXXXXXXXXXXXXXXXFXXXXXXXXXXXXXXXXXXXFGSMRRSPVDYRKDISRSRAISPPRKEYVMRDISPRNRDISPRMRDIEXXXXXXXXXXXXXXXXXXXXXXXSRNFESRNRDGRRDYSPNAR 617
            PFNKFEDRSPKEDFPERGFRVSRRPIGNFSKNYSRDEYRQRDERRDSYERDSFRQRESRRDPRERLRGRDREFGSMRRSPVDYRKDISRSRAISPPRKEYVMRDISPRNRDISPRMRDIEPRIRDMEPRMRDMDPRFRDYPPRSRNFESRNRDGRRDYSPNAR
Sbjct:   25 PFNKFEDRSPKEDFPERGFRVSRRPIGNFSKNYSRDEYRQRDERRDSYERDSFRQRESRRDPRERLRGRDREFGSMRRSPVDYRKDISRSRAISPPRKEYVMRDISPRNRDISPRMRDIEPRIRDMEPRMRDMDPRFRDYPPRSRNFESRNRDGRRDYSPNAR 187
The following BLAST results are available for this feature:
BLAST of SMED30025141 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30025141 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30025141 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30025141 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30025141 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30025141 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30025141 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30025141 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30025141 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30025141 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30025141 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30025141 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30025141 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30025141 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 4
Match NameE-valueIdentityDescription
SMESG000076211.11.845e-126100.00SMESG000076211.1[more]
SMESG000076211.14.273e-91100.00SMESG000076211.1[more]
SMESG000047610.12.087e-73100.00SMESG000047610.1[more]
SMESG000047610.18.231e-48100.00SMESG000047610.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30025141 ID=SMED30025141|Name=SMED30025141|organism=Schmidtea mediterranea sexual|type=transcript|length=1893bp
CGATCTGTAAGTTTCCATCTTTATTTATTTGTTATATTTTGCTAGAATTA
TTGTAGATGAGTTACGATAGGTCATTTTCAAGAGGCAGAGGTCGTGGTAG
GGGTGGATTTAATGATAGTGGATCCCGGCCATTTAATAAATTTGAAGATC
GGTCTCCTAAAGAGGATTTTCCTGAACGAGGCTTTAGAGTATCTCGTAGA
CCAATTGGCAATTTTTCTAAAAATTATAGTCGTGATGAATATAGACAAAG
AGATGAAAGACGTGACAGTTATGAAAGAGATTCATTTAGACAAAGAGAAA
GTCGCAGAGATCCAAGAGAGCGATTACGAGGCAGAGATAGAGAATTTGGT
AGTATGAGACGAAGTCCAGTTGACTATCGCAAGGATATATCTCGTAGTCG
TGCTATTTCACCTCCACGGAAAGAATATGTTATGAGGGACATTTCACCTA
GGAATCGAGATATATCACCTCGTATGAGAGACATTGAACCAAGAATTAGA
GACATGGAACCAAGAATGAGAGATATGGATCCTAGATTTCGAGATTATCC
ACCAAGATCTAGAAATTTTGAAAGTAGAAATCGTGATGGTCGTAGAGATT
ACTCGCCTAATGCGAGAGACAGACATTTTTCTCCTGTCAGGTATCAACAC
GATCGTTATGAATATAGTCCTCCTAGGAGCAGAAATTATGAGCGAGAAAG
CTTTCCTGATAGAAGACGCAATGACGTGAGATCTTTTAATTCAAGAGAAA
ATAGAGAATATCGATCTAGAAGCCCCAATAATTTTCGGCCCCGTGGTGGT
CGATTTAATAGTCAACGAGGCAATACTCGGGGGCGAGATAATTTAAATCG
ATTTGATTCGAATCAGAGAAATAATTTTAATCGCGCAAGAGATGAGTCTT
CTATGAGAAGAGGACATAATAATGATAATCCAAAGAGGAAAGTTGAGCAA
GTGCCTAATTCTGGAATTCCACCACAAAAGAAAAGTCGTGACAGTTCTTT
TGATACAAGTCCATAAGAATTGTTGTTTAATTCATTACTTGTTGTCAATA
AATCCATAAAATATTGTTAATTATGTTTGTCGAATTCAATGCAAAAATGC
ATTTTCAAATTTAATAAATGTTATTTAAAGATGCAGAAGCTCAGATTTAA
CAAAGAAATTAGTTTCGATCGCCATATTGAAATAACCTCTCAATGTTATG
ATAGATAACTTAAACCGAATATTGAAAATAAATTGCAGCAATACGTTTTG
GGAAAATTAATTCGCACAGAACTGCTCAAATTCGAAGTATCGAATATCTT
AATTAATATTCTAAATAGAAGAAAACCTTGGCTACCTTAGTTTTTTGAGT
CGATTCTATTATGAAATCATCACGATCAGATTGCTATGAATTTGATTCTT
TCTAGTAAAAATTAAAGTTAAAGAAAATCGAAATAAGTGCAAATGTTTAT
TAAGTATTTTAGAAGTTATTAAGCTAAGTAAATATTATTATGCTACACTT
ACTCACCTGTTTATTCTCCATATTGGTATTTAAATAGTCATTACATTTGT
ATCAAAAGGAAGAAAATGATTTTGAAAGTAATTCTAGTGGTGAGTGATAG
TTTATATGCAAACTGCAGTTATGATGGGTGATGAATTAATTTTTTGTTTT
GATTATGGAGCTATTTATATTTTTTGTTTGTATATTGGGATTCAGGTTTA
ATCAATCAAGAGTAAATTATATGCTATGCGAAGAACTACATGCACTTTAA
AGTTGCAATAAATTTTTTTATTTTTGTGTTTTTTGAAATAATCTTACTAA
AAATTTGATTAAATTTTGTGTTTAGTTGGATTTAAGAGTTTGTTTTTAAC
TGATTTATACTAAATCCAAAAATGATTTTCATTGTGTGACAAA
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protein sequence of SMED30025141-orf-1

>SMED30025141-orf-1 ID=SMED30025141-orf-1|Name=SMED30025141-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=320bp
MSYDRSFSRGRGRGRGGFNDSGSRPFNKFEDRSPKEDFPERGFRVSRRPI
GNFSKNYSRDEYRQRDERRDSYERDSFRQRESRRDPRERLRGRDREFGSM
RRSPVDYRKDISRSRAISPPRKEYVMRDISPRNRDISPRMRDIEPRIRDM
EPRMRDMDPRFRDYPPRSRNFESRNRDGRRDYSPNARDRHFSPVRYQHDR
YEYSPPRSRNYERESFPDRRRNDVRSFNSRENREYRSRSPNNFRPRGGRF
NSQRGNTRGRDNLNRFDSNQRNNFNRARDESSMRRGHNNDNPKRKVEQVP
NSGIPPQKKSRDSSFDTSP*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000099neuron
PLANA:0000429neoblast
PLANA:0002032epidermal cell
PLANA:0002109X1 cell
PLANA:0002111X2 cell
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 303..319
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 272..294
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 244..259
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 58..240
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 25..44
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 1..319